Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing
Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing
Background: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.
Results: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.
Conclusions: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.
Antibiotics, Antimicrobial resistant bacteria, DNA stable isotope probing, High-throughput sequencing, Metagenomics, Pathogens, Soil
Hernández, Marcela
e73477e7-cf3e-4f50-97c8-4494c5b05cd0
Roy, Shamik
5d8fc687-2d5a-4dc1-8d41-03527abba26d
Keevil, C. William
cb7de0a7-ce33-4cfa-af52-07f99e5650eb
Dumont, Marc G.
afd9f08f-bdbb-4cee-b792-1a7f000ee511
18 April 2023
Hernández, Marcela
e73477e7-cf3e-4f50-97c8-4494c5b05cd0
Roy, Shamik
5d8fc687-2d5a-4dc1-8d41-03527abba26d
Keevil, C. William
cb7de0a7-ce33-4cfa-af52-07f99e5650eb
Dumont, Marc G.
afd9f08f-bdbb-4cee-b792-1a7f000ee511
Hernández, Marcela, Roy, Shamik, Keevil, C. William and Dumont, Marc G.
(2023)
Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing.
Environmental Microbiome, 18 (1), [34].
(doi:10.1186/s40793-023-00489-7).
Abstract
Background: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.
Results: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.
Conclusions: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.
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Hernandez-et-al
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s40793-023-00489-7
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Accepted/In Press date: 28 March 2023
Published date: 18 April 2023
Additional Information:
Funding Information:
This work was funded by a Natural Environmental Research Council (NERC, UK) award to Marc G. Dumont and C. William Keevil (NE/N02026X/1). Shamik Roy was supported by a NERC Discipline Hopping (DH) for Discovery Science grant awarded to Marcela Hernández (NE/X018180/1). Marcela Hernández was also supported by a Royal Society Dorothy Hodgkin Research Fellowship (DHF\R1\211076).
Funding Information:
The authors thank Mike Cotton (University of Southampton) for helping with soil sampling.
Publisher Copyright:
© 2023, The Author(s).
Keywords:
Antibiotics, Antimicrobial resistant bacteria, DNA stable isotope probing, High-throughput sequencing, Metagenomics, Pathogens, Soil
Identifiers
Local EPrints ID: 477060
URI: http://eprints.soton.ac.uk/id/eprint/477060
ISSN: 2524-6372
PURE UUID: 73cac2a4-f76a-40cf-ba2d-f5ab49ac0d02
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Date deposited: 25 May 2023 16:37
Last modified: 17 Mar 2024 03:40
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Author:
Marcela Hernández
Author:
Shamik Roy
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